The character compatibility approach, which removes all homoplasic characters and involves finding the largest clique of compatible characters in a dataset, in principle, provides a powerful means ...for obtaining correct topology in difficult to resolve cases. However, the usefulness of this approach to generalized molecular sequence data for phylogeny determination has not been studied in the past. We have used this approach to determine the topology of 23 proteobacterial species (6 each of alpha-, beta- and gamma-, 3 delta-, and 2 epsilon-proteobacteria) using sequence data for 10 conserved proteins (Hsp60, Hsp70, EF-Tu, EF-G, alanyl-tRNA synthetase, RecA, GyrA, GyrB, RpoB and RpoC). All sites in the sequence alignments of these proteins where only two amino acids were found, with each amino acid present in at least two species, were selected. Mutual compatibility determination on these binary state sites was carried out by two means. In one case, all of these sites were combined into a large dataset (Set A; 957 characters) prior to compatibility analysis. In the second case, compatibility analysis was carried out on characters from individual proteins and all compatible sites were combined into a large dataset (Set B; 398 characters) for further studies. Upon compatibility analyses, the largest cliques that were obtained from Sets A and B consisted of 337 and 323 compatible characters, respectively. In these cliques, all proteobacterial subgroups were clearly distinguished and branching orders of most of the species were also resolved. The epsilon-proteobacteria exhibited the earliest branching, whereas the beta- and gamma-subgroups were found to have emerged last. The relative placement of the alpha- and delta-subgroups, however, was not resolved. The topology of these species was also determined based on 16S rRNA sequences and a concatenated dataset of sequences for all 10 proteins by means of neighbor-joining, maximum likelihood, and maximum parsimony methods. In the protein trees, all proteobacterial groups were reliably resolved and they branched in the following order: (epsilon(delta(alpha(beta,gamma))). However, in the rRNA trees, the gamma- and beta-subgroups exhibited polyphyletic branching and many internal nodes were not resolved. These results indicate that the character compatibility analysis using generalized molecular sequence data provides a powerful means for evolutionary studies. Based on molecular sequences, it should be possible to obtain very large datasets of compatible characters that should prove very helpful in clarifying difficult to resolve phylogenetic relationships.
Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK
Correspondence P. H. A. Sneath ( phas1{at}le.ac.uk )
ABSTRACT
To celebrate the 25th anniversary of ...the publication of the Approved Lists of Bacterial Names in 1980, the surviving editor Peter Sneath reflects on the conception, preparation and publication of this seminal document in the nomenclature of not just prokaryotes but all organisms.
The MUon Scattering Experiment, MUSE, at the Paul Scherrer Institute, Switzerland, investigates the proton charge radius puzzle, lepton universality, and two-photon exchange, via simultaneous ...measurements of elastic muon-proton and electron-proton scattering. The experiment uses the PiM1 secondary beam channel, which was designed for high precision pion scattering measurements. We review the properties of the beam line established for pions. We discuss the production processes that generate the electron and muon beams, and the simulations of these processes. Simulations of the π/μ/e beams through the channel using TURTLE and G4beamline are compared. The G4beamline simulation is then compared to several experimental measurements of the channel, including the momentum dispersion at the intermediate focal plane and target, the shape of the beam spot at the target, and timing measurements that allow the beam momenta to be determined. Finally, we conclude that the PiM1 channel can be used for high precision π, μ, and e scattering.
Four hundred and seventy-five strains, which included 394 type cultures of Streptomyces and representatives of 14 other actinomycete genera, were studied. Overall similarities of these strains for ...139 unit characters were determined by the SSM and SJ coefficients and clustering by the UPGMA algorithm. Test error and overlap between the phena defined were within acceptable limits. Cluster-groups were defined by the SSM coefficient at the 70.1% similarity (S) level and by the SJ coefficient at the 50% S-level. Clusters were distinguished at the 77.5% SSM and 63% SJ S-levels. Groupings obtained with the two coefficients were generally similar, but there were some changes in the definition and membership of cluster-groups and clusters. The phenetic data obtained, together with those from previous diverse studies, indicated that the genera Actinopycnidium, Actinosporangium, Chainia, Elytrosporangium, Kitasatoa and Microellobosporia should be reduced to synonyms of Streptomyces, while Intrasporangium, Nocardioides and Streptoverticillium remained as distinct genera in the family Streptomycetaceae. Nocardiopsis dassonvillei also showed strong phenetic affinity to Streptomyces, despite its chemotaxonomic differences. Actinomadura sensu stricto was phenetically distinguishable from Streptomyces and 'Nocardia' mediterranea was recognized as a taxon distinct from both these genera and from Nocardia sensu stricto. Most of the Streptomyces type cultures fell into one large cluster-group. At the 77.5% SSM S-level, they were recovered in 19 major and 40 minor clusters, with 18 strains recovered as single member clusters. The status of the latter as species was therefore confirmed. Most of the minor clusters, consisting of two to five strains, can also be regarded as species. The major clusters varied in size (from 6 to 71 strains) and in there homogeneity. Therefore, it is suggested that they be regarded as species-groups until further information is available. The results provide a basis for the reduction of the large number of Streptomyces species which have been described. They also demonstrate that the previous use of a limited number of subjectively chosen characters to define species-groups or species has resulted in artificial classifications.
Estimates of the final size of the variant Creuzfeldt-Jakob Disease epidemic have been made by fitting theoretical curves of the incubation period distribution to the histogram of observed annual ...deaths to 2002, using various assumptions of the mean and standard deviation of this distribution, and also of the efficacy of the Specified Bovine Offals ban of 1989. Unless the mean incubation time is greater than 15 to 20 years the estimates lie in the low hundreds to about a thousand, and the most likely situation, of a mean between 11 and 15 years, gives estimates of about 150 to 500 deaths. Numbers above a few thousands would only occur if the mean incubation period is of the order of 25 to 30 years and reasons are adduced to indicate this is very unlikely. These numbers are not greatly increased if the ban was poorly observed. This method of analysis may be applicable to other situations where a cause that is limited in space and time is expected to have late effects.
The character state data obtained for clusters defined at the 77.5% SSM similarity level in the phenetic numerical classification described by Williams et al. (1983) were used to construct a ...probabilistic identification matrix. The 23 phena included were the major clusters (19 Streptomyces, 2 Streptoverticillium and 'Nocardia' mediterranea) and one minor cluster (Streptomyces fradiae). The characters most diagnostic for these clusters were selected using Sneath's CHARSEP and DIACHAR programs. The resulting matrix consisted of 41 characters x 23 phena. Identification scores, determined by Sneath's MATIDEN program were used to evaluate the matrix. Theoretical assessment was achieved by determination of the cluster overlap (OVERMAT), the identification scores for the Hypothetical Medium Organism of each cluster (MOSTTYP), and the scores for randomly selected cluster representatives using the classification data of Williams et al. (1983). The matrix was evaluated practically by the independent re-determination of the characters for the same cluster representatives, which also provided a measure of test error. Finally it was used to identify unknown isolates from a range of habitats. The results showed that the matrix was theoretically sound. Test error was within acceptable limits and did not distort identifications. Of the unknown isolates, 80% were clearly identified with a cluster. It is suggested that the matrix could form the basis for a more objective identification and grouping of the large number of Streptomyces species which have been described.
Conventionally, small populations living on islands are expected to lose genetic variation by drift. Fluctuations in population size, combined with polygynous mating systems, are expected to ...contribute to the process by increasing sampling effects on genetic variation. However, in individually monitored populations of Red deer on Rum and Soay sheep on St. Kilda, which experience fluctuations in population size, two processes have been identified which mitigate loss of genetic variation. First, in a number of examples, population reductions are associated with selection. Selection may be in favour of heterozygotes, or, as we have documented in several cases, it may fluctuate in direction temporally. Second, in Soay sheep, in which mortality over population crashes is male-biased, ostensibly leading to low effective numbers of males, molecular studies show that there are systematic changes in the reproductive success of young males, and in variance in male success, that broaden genetic representation compared with expectation.
A numerical phenotypic taxonomic study of 315 strains of Neisseria and some allied bacteria examined for 155 phenotypic tests showed 31 groups, most of which were reasonably distinct. These fell into ...four major areas. Areas A, B and C contained species of Neisseria, whereas area D contained the organisms known as 'false neisserias' together with Branhamella, Moraxella and Kingella species. Area A contained N. gonorrhoeae (which showed two subgroups), N. meningitidis (with two subgroups, and N. cinerea closely associated), N. polysaccharea, N. elongata subsp, glycolytica and N. lactamica. Area B contained mainly organisms from the human nasopharynx, and the nine groups were not very distinct: only three, N. mucosa, N. perflava and N. sicca could be recognized by the presence of type strains, and there was little relationship between taxonomic position and species epithets. Area C contained several groups from animals, N. animalis, N. canis and two phenons that may be justified as new species of Neisseria, one from lizards and the other from dental plaque of herbivores. Area C also contained N. elongata, N. subflava (with N. flavescens), type strain of Morococcus cerebrosis and the CDC groups M-5 (N. weaveri) and EF-4. Area D contained Branhamella catarrhalis, a combined group which consists of strains of the 'false neisserias' N. caviae and N. cuniculi, the 'false neisseria' N. ovis, and a group of Moraxella strains. A small group representing Kingella kingae is included in area D. Mean test error was 1.7%.
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